Package | Description |
---|---|
com.compomics.cli.modifications |
Command line for the handling of modifications.
|
com.compomics.util.experiment.biology.modifications | |
com.compomics.util.experiment.biology.proteins |
Classes related to proteins.
|
com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
|
com.compomics.util.experiment.identification.modification |
Additional PSM scoring classes.
|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.gui.modification |
PTM GUI dialogs.
|
com.compomics.util.parameters.identification.search |
Identification parameters relative to the search.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationsCLIInputBean.getModificationToAdd()
Returns the modification to add.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationFactory.getModification(String name)
Returns the Modification indexed by its name.
|
static Modification |
ModificationFactory.getSingleAAModification(Modification modification)
Returns a clone of the given Modification targeting a single amino acid instead of
a pattern.
|
Modification |
ModificationFactory.getSingleAAModification(String modificationName)
Returns a clone of the given Modification targeting a single amino acid instead of
a pattern.
|
Modifier and Type | Method and Description |
---|---|
void |
ModificationFactory.addUserModification(Modification modification)
Adds a new user modification.
|
static Modification |
ModificationFactory.getSingleAAModification(Modification modification)
Returns a clone of the given Modification targeting a single amino acid instead of
a pattern.
|
boolean |
Modification.isSameAs(Modification anotherPTM)
Returns true if the PTM is the same as another one.
|
boolean |
Modification.isSameAtomicComposition(Modification anotherPTM)
Returns true if the atomic composition of the PTM is the same as another
one.
|
boolean |
Modification.isSamePattern(Modification anotherPTM)
Returns true if the targeted pattern of the PTM is the same as another
one.
|
Modifier and Type | Method and Description |
---|---|
HashSet<Integer> |
Peptide.getPotentialModificationSites(Modification modification,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as a set.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(Modification modification,
String proteinSequence,
int peptideStart,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of sites.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSitesNoCombination(Modification modification,
String proteinSequence,
int peptideStart)
Returns the potential modification sites as an ordered list of sites.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(Modification modification,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationPreferences,
SpecificAnnotationParameters specificAnnotationPreferences)
Returns the modification plot series in the JFreechart format for one
PSM.
|
static ModificationtableContent |
ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationParameters)
Get the table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
void |
FMIndex.addModificationPattern(Modification modification)
Adds a modification pattern for bitwise pattern search.
|
Constructor and Description |
---|
ModificationDialog(JDialog parent,
Modification currentModification,
boolean editable)
Creates a new Modification dialog.
|
ModificationDialog(JFrame parent,
PtmToPrideMap modificationToPrideMap,
Modification currentModification,
boolean editable)
Creates a new Modification dialog.
|
ModificationTable(Identification identification,
AnnotationParameters annotationParameters,
PeptideMatch peptideMatch,
Modification ptm,
boolean areaChart)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Modification |
ModificationParameters.getModification(String modName)
Returns the back-ed up modification with the given name.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,Modification> |
ModificationParameters.getBackedUpModifications()
Returns the modifications backed-up as a map.
|
Modifier and Type | Method and Description |
---|---|
void |
ModificationParameters.addFixedModification(Modification modification)
Adds a fixed modification.
|
void |
ModificationParameters.addRefinementFixedModification(Modification modification)
Adds a fixed refinement modification.
|
void |
ModificationParameters.addRefinementVariableModification(Modification modification)
Adds a variable refinement modification.
|
void |
ModificationParameters.addVariableModification(Modification modification)
Adds a variable modification.
|
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